; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.164326_pwKcuY.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return pval -uth pval 0.001 -i $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.164326_QDn9MI.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.164326_QDn9MI.fasta ; bg $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.164326_pwKcuY.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method file ; Markov order 1 ; Strand sensitive ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.34589 ; c 0.15671 ; g 0.15366 ; t 0.34374 ; Thresholds lower upper ; pval NA 0.001 ; Output columns ; 1 seq_id ; 2 ft_type ; 3 ft_name ; 4 strand ; 5 start ; 6 end ; 7 sequence ; 8 weight #seq_id ft_type ft_name strand start end sequence weight Pval ln_Pval sig AT1G76440 limit START_END D -500 -1 . 0 0 0 0 GWD2 limit START_END D -500 -1 . 0 0 0 0 AT3G13340 limit START_END D -500 -1 . 0 0 0 0 AT4G10895 limit START_END D -500 -1 . 0 0 0 0 AT1G07317 limit START_END D -500 -1 . 0 0 0 0 AT2G28010 limit START_END D -500 -1 . 0 0 0 0 AT3G50540 limit START_END D -500 -1 . 0 0 0 0 AT1G07485 limit START_END D -500 -1 . 0 0 0 0 AT1G56880 limit START_END D -500 -1 . 0 0 0 0 ARR18 limit START_END D -500 -1 . 0 0 0 0 AT3G18230 limit START_END D -500 -1 . 0 0 0 0 RALFL16 limit START_END D -500 -1 . 0 0 0 0 AT5G12940 limit START_END D -500 -1 . 0 0 0 0 AT5G28450 limit START_END D -500 -1 . 0 0 0 0 AT3G61680 limit START_END D -500 -1 . 0 0 0 0 AT3G03695 limit START_END D -500 -1 . 0 0 0 0 AT1G29480 limit START_END D -500 -1 . 0 0 0 0 AT2G38185 limit START_END D -500 -1 . 0 0 0 0 PCMP-H40 limit START_END D -500 -1 . 0 0 0 0 AT1G20430 limit START_END D -500 -1 . 0 0 0 0 AT1G10790 limit START_END D -500 -1 . 0 0 0 0 AT5G03820 limit START_END D -500 -1 . 0 0 0 0 AT1G74780 limit START_END D -500 -1 . 0 0 0 0 AT2G20873 limit START_END D -500 -1 . 0 0 0 0 AT2G08815 limit START_END D -500 -1 . 0 0 0 0 FBL4 limit START_END D -500 -1 . 0 0 0 0 AT5G35475 limit START_END D -500 -1 . 0 0 0 0 EDL2 limit START_END D -500 -1 . 0 0 0 0 AT1G76440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -211 -204 TTACCTGC 5.2 5.9e-04 -7.435 3.229 GWD2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -493 -486 TTCCCTGC 4.8 8.8e-04 -7.036 3.056 AT1G07317 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -333 -326 TATCTCGC 5.7 3.4e-04 -7.987 3.469 AT1G07317 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -271 -264 TTTACCGC 7.6 4.7e-05 -9.965 4.328 AT2G28010 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -118 -111 ATTCCCCC 6.3 2.9e-04 -8.146 3.538 AT1G56880 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -319 -312 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 ARR18 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -357 -350 TTACTCGC 5.6 3.5e-04 -7.958 3.456 ARR18 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -164 -157 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT5G12940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -429 -422 TGTCCCTC 4.9 8.8e-04 -7.036 3.056 AT5G12940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -267 -260 TCTCCCGA 5.1 6.7e-04 -7.308 3.174 AT5G28450 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -119 -112 TTCCTCGC 5.2 5.9e-04 -7.435 3.229 AT3G61680 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -404 -397 TTACCCGT 5.3 5.1e-04 -7.581 3.292 AT3G61680 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -363 -356 TCTCACGC 5.4 4.2e-04 -7.775 3.377 AT3G03695 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -392 -385 TTTCCTGC 7.1 1.4e-04 -8.874 3.854 AT1G29480 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -224 -217 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 AT2G38185 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -24 -17 ATACCCTC 4.7 9.5e-04 -6.959 3.022 PCMP-H40 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -497 -490 ATACCAGC 4.9 8.8e-04 -7.036 3.056 AT1G20430 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -473 -466 TTGCCCAC 4.7 9.5e-04 -6.959 3.022 AT1G20430 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -311 -304 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 AT1G10790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -272 -265 TTACCCGC 8.3 1.8e-05 -10.925 4.745 AT1G74780 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -257 -250 TCTCCCGC 8.2 1.9e-05 -10.871 4.721 AT2G20873 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -435 -428 TATACCGC 5.9 3.1e-04 -8.079 3.509 AT2G20873 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -329 -322 TATCCCAC 5.1 6.7e-04 -7.308 3.174 AT2G20873 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -128 -121 TGTTCCGC 5.1 6.7e-04 -7.308 3.174 AT2G08815 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -441 -434 TTCCACGC 5.1 6.7e-04 -7.308 3.174 AT2G08815 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -426 -419 CTTCCTGC 5.3 5.1e-04 -7.581 3.292 AT2G08815 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -323 -316 TCTCCCAC 4.9 8.8e-04 -7.036 3.056 AT5G35475 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -216 -209 TATCACGC 5.6 3.5e-04 -7.958 3.456 AT1G76440 site 5015_E2Fb_Athamap_20091028_ D -211 -204 TTACCTGC 5.1 5.8e-04 -7.452 3.237 GWD2 site 5015_E2Fb_Athamap_20091028_ R -493 -486 TTCCCTGC 4.7 7.9e-04 -7.143 3.102 AT1G07317 site 5015_E2Fb_Athamap_20091028_ D -333 -326 TATCTCGC 5.6 3.3e-04 -8.016 3.481 AT1G07317 site 5015_E2Fb_Athamap_20091028_ D -271 -264 TTTACCGC 7.8 3.7e-05 -10.205 4.432 AT2G28010 site 5015_E2Fb_Athamap_20091028_ D -118 -111 ATTCCCCC 6.2 2.9e-04 -8.146 3.538 AT1G56880 site 5015_E2Fb_Athamap_20091028_ D -319 -312 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 ARR18 site 5015_E2Fb_Athamap_20091028_ R -357 -350 TTACTCGC 5.5 3.6e-04 -7.929 3.444 ARR18 site 5015_E2Fb_Athamap_20091028_ D -164 -157 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT5G12940 site 5015_E2Fb_Athamap_20091028_ D -429 -422 TGTCCCTC 4.8 7.5e-04 -7.195 3.125 AT5G12940 site 5015_E2Fb_Athamap_20091028_ R -267 -260 TCTCCCGA 5.0 6.5e-04 -7.339 3.187 AT5G28450 site 5015_E2Fb_Athamap_20091028_ D -119 -112 TTCCTCGC 5.1 5.8e-04 -7.452 3.237 AT3G61680 site 5015_E2Fb_Athamap_20091028_ D -404 -397 TTACCCGT 5.2 5.1e-04 -7.581 3.292 AT3G61680 site 5015_E2Fb_Athamap_20091028_ D -363 -356 TCTCACGC 5.3 4.4e-04 -7.729 3.357 AT3G03695 site 5015_E2Fb_Athamap_20091028_ D -392 -385 TTTCCTGC 7.3 1.3e-04 -8.948 3.886 AT3G03695 site 5015_E2Fb_Athamap_20091028_ R -67 -60 TTTAACGC 4.5 9.4e-04 -6.970 3.027 AT1G29480 site 5015_E2Fb_Athamap_20091028_ R -224 -217 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT1G20430 site 5015_E2Fb_Athamap_20091028_ R -473 -466 TTGCCCAC 4.7 8.2e-04 -7.106 3.086 AT1G20430 site 5015_E2Fb_Athamap_20091028_ R -311 -304 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 AT1G10790 site 5015_E2Fb_Athamap_20091028_ D -272 -265 TTACCCGC 8.5 1.8e-05 -10.925 4.745 AT1G74780 site 5015_E2Fb_Athamap_20091028_ R -257 -250 TCTCCCGC 8.4 2.1e-05 -10.771 4.678 AT2G20873 site 5015_E2Fb_Athamap_20091028_ R -435 -428 TATACCGC 5.8 3.1e-04 -8.079 3.509 AT2G20873 site 5015_E2Fb_Athamap_20091028_ R -329 -322 TATCCCAC 5.1 6.5e-04 -7.339 3.187 AT2G20873 site 5015_E2Fb_Athamap_20091028_ R -128 -121 TGTTCCGC 5.1 6.5e-04 -7.339 3.187 AT2G08815 site 5015_E2Fb_Athamap_20091028_ D -441 -434 TTCCACGC 5.1 6.5e-04 -7.339 3.187 AT2G08815 site 5015_E2Fb_Athamap_20091028_ D -426 -419 CTTCCTGC 5.2 5.1e-04 -7.581 3.292 AT2G08815 site 5015_E2Fb_Athamap_20091028_ D -365 -358 TTCCCCTC 4.6 8.2e-04 -7.106 3.086 AT2G08815 site 5015_E2Fb_Athamap_20091028_ D -323 -316 TCTCCCAC 4.8 7.5e-04 -7.195 3.125 AT5G35475 site 5015_E2Fb_Athamap_20091028_ R -216 -209 TATCACGC 5.6 3.3e-04 -8.016 3.481 AT3G13340 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -427 -417 GAGCCGCGCTA 5.1 5.4e-04 -7.524 3.268 AT2G28010 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -358 -348 TTCCTACGAAA 4.4 9.8e-04 -6.928 3.009 AT2G28010 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -300 -290 TTCCTACCAAA 5.0 6.0e-04 -7.419 3.222 AT2G28010 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -270 -260 TTCCTACGAAA 4.4 9.8e-04 -6.928 3.009 AT3G50540 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -134 -124 ATCCCGAGAAG 4.5 9.1e-04 -7.002 3.041 AT1G56880 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -318 -308 TTCCCACTCTG 4.6 8.3e-04 -7.094 3.081 ARR18 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -361 -351 TACTCGCAAAT 5.0 6.5e-04 -7.339 3.187 ARR18 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -163 -153 TAACCGCGTAA 5.2 5.4e-04 -7.524 3.268 AT3G18230 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -212 -202 TTGCCGACAAA 5.1 5.4e-04 -7.524 3.268 AT5G28450 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -401 -391 CTCTCGCCATT 6.0 2.7e-04 -8.217 3.569 AT3G61680 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -238 -228 CTCCAGCGCAA 5.8 3.1e-04 -8.079 3.509 AT3G61680 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -64 -54 TACGCGCGGTT 6.9 1.3e-04 -8.948 3.886 AT3G03695 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -391 -381 TTCCTGCCACA 6.3 2.3e-04 -8.377 3.638 AT3G03695 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -266 -256 TTTACGCCAAT 5.4 4.2e-04 -7.775 3.377 AT3G03695 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -140 -130 TGCGTGCCATT 4.5 9.1e-04 -7.002 3.041 AT1G29480 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -228 -218 TTCCCTCAAAT 5.0 6.0e-04 -7.419 3.222 AT1G10790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -339 -329 CCCCCGCGAAT 6.0 2.7e-04 -8.217 3.569 AT1G10790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -271 -261 TACCCGCGGTT 7.6 6.6e-05 -9.626 4.180 AT1G10790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -41 -31 ATCCCACTATT 5.4 4.2e-04 -7.775 3.377 AT1G74780 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -261 -251 CTCCCGCAAAT 6.4 1.9e-04 -8.568 3.721 AT2G20873 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -333 -323 ATCCCACGCTA 7.1 1.1e-04 -9.115 3.959 AT2G08815 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -440 -430 TCCACGCCAAT 6.2 2.5e-04 -8.294 3.602 AT2G08815 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -425 -415 TTCCTGCTCTC 4.9 6.5e-04 -7.339 3.187 FBL4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -123 -113 ATTCCGCCAAA 7.4 8.1e-05 -9.421 4.092 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 8 4 0 -11.100 10.500 21.600 a:0.346 c:0.157 g:0.154 t:0.344 ; 2 5015_E2Fb_Athamap_20091028_ 8 4 0 -12.900 10.900 23.800 a:0.346 c:0.157 g:0.154 t:0.344 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 11 4 0 -19.800 12.800 32.600 a:0.346 c:0.157 g:0.154 t:0.344 ; Number of sequences scanned 28 ; Sum of sequence lengths 14000 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 28 0 ; 2 5015_E2Fb_Athamap_20091028_ 28 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 24 0 ; TOTAL 80 0 ; Host name rsat ; Job started 2026-08-17.164327 ; Job done 2026-08-17.164328 ; Seconds 0.5 ; user 0.5 ; system 0.03 ; cuser 0.77 ; csystem 0.11